--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sRbowtieParser.py	Wed May 27 17:19:15 2015 -0400
@@ -0,0 +1,57 @@
+#!/usr/bin/python
+# python parser module to analyse sRbowtie alignments
+# version 1.0.2 - argparse implementation
+# Usage sRbowtieParser.py  <1:index source> <2:extraction directive> <3:outputL> <4:polarity> <5:6:7 filePath:FileExt:FileLabel> <.. ad  lib>
+
+import sys, argparse
+from smRtools import *
+
+def masterListGenerator(data_source):
+  for filePath, FileExt, FileLabel in data_source:
+    yield HandleSmRNAwindows (filePath, FileExt, IndexSource, genomeRefFormat)
+
+def Parser():
+  the_parser = argparse.ArgumentParser()
+  the_parser.add_argument('--IndexSource', action="store", type=str, help="Path to the index source")
+  the_parser.add_argument('--ExtractDirective', action="store", type=str, choices=["fastaSource", "bowtieIndex"], help="Extract info from fasta or bowtie index")
+  the_parser.add_argument('--output', action="store", type=str, help="path to the output")
+  the_parser.add_argument('--polarity', choices=["forward", "reverse", "both"], help="forward, reverse or both forward an reverse reads are counted")
+  the_parser.add_argument('--alignmentSource',nargs='+', help="paths to alignments files")
+  the_parser.add_argument('--alignmentFormat',nargs='+', help="Format of the bowtie alignment (tabular, sam or bam)")
+  the_parser.add_argument('--alignmentLabel',nargs='+', help="Label of the alignment")
+  args = the_parser.parse_args()
+  return args
+
+args = Parser()
+
+IndexSource = args.IndexSource
+genomeRefFormat = args.ExtractDirective
+Output = args.output
+Polarity = args.polarity
+header = ["gene"]
+
+
+FileLabelList=[label for label in args.alignmentLabel]
+header.extend(FileLabelList)
+assert (len(FileLabelList)==len(set(FileLabelList))),"You have supplied a non-unique label. Please make sure that your input files have unique names"
+
+data_source=zip (args.alignmentSource, args.alignmentFormat, args.alignmentLabel)
+master_generator=masterListGenerator(data_source)
+
+for i,window in enumerate(master_generator):
+  window=window
+  if i==0:
+    gene_count_dict={gene:[str(item.readcount(polarity=Polarity))] for gene,item in window.instanceDict.items()}
+  else:
+    [gene_count_dict[gene].append(str(item.readcount(polarity=Polarity))) for gene,item in window.instanceDict.items()]
+
+
+F = open (args.output, "w")
+# print >>F, args
+print >> F, "\t".join(header)
+
+for item in sorted(gene_count_dict.keys()):
+  line=[item]
+  line.extend(gene_count_dict[item])
+  print >> F,  "\t".join(line )
+F.close()